Could you explain your set-up in a bit more detail, because I'm having some trouble following you...or where you are in this switch you describe.
It sounds like you are saying that your "Work folder" is excluded from Time machine backups. Is this folder on your Mac or on your NAS? If on your Mac, is it also currently the a folder you have associated to Dropbox? If it is a folder on your Mac, not being able to reverse the exclusion is a problem to be addressed. If on your NAS, I don't believe Time Machine normally backs up SMB shares (how would it given how the hard links and snapshots for TM work?).
Similarly, where are your currently backing up to with Time Machine? The NAS? If so that is a problem - but one related to the 3-2-1 backup model and good practice, because if the NAS fails, your Work folder and your backups go down together, which is bad news.
If the NAS is not your backup server, then the question of versioning on the NAS depends on whether the NAS natively supports version controls in files, or has an app in their store for adding that on. Snapshots will give you something similar, but NAS snapshots in my experience are far less efficient than Time Machine (much larger and eat up disk space more quickly, so less versions can be stored).
